MERFISH Report

1. Overview

  • Principle Investigator: Mehrdad Shamloo

  • Institution: Stanford

  • Project: SPR22-003 Aged Sleep Deprivation study

1.1 Slice Submission

This is the detailed slice information we got from collaborators:

Sample ID Anatomical source Preparation method Treatments Species & Genetic background Sex Age
1 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 18 months mouse c57bl6 m 18 mo
2 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 18 months mouse c57bl7 m 18 mo
3 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 18 months mouse c57bl8 m 18 mo
23 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 18 months mouse c57bl9 m 18 mo
24 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 18 months mouse c57bl10 m 18 mo
25 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 18 months mouse c57bl11 m 18 mo
31 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl12 m 4 mo
32 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl13 m 4 mo
33 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl14 m 4 mo
34 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl15 m 4 mo
35 brain hemisphere perfused and flash frozen in OCT embedding media No Sleep Deprivation- 4 months mouse c57bl16 m 4 mo
36 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl17 m 4 mo
37 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl18 m 4 mo
38 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl19 m 4 mo
39 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl20 m 4 mo
40 brain hemisphere perfused and flash frozen in OCT embedding media Sleep Deprivation- 4 months mouse c57bl21 m 4 mo

1.2 Sample Information

A brief sample information is generated from the submission table for the following analysis.

“SD” refers to “Sleep Deprivation” while “nSD” refers to “No Sleep Deprivation”.

Sample Index and Basic Information
Batch Index Genotype region Mice Age (month) Data Path
1 nSD1 nSD region_0 18 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101
1 SD23 SD region_1 18 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101
2 nSD2 nSD region_0 18 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201
2 SD24 SD region_1 18 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201
3 nSD3 nSD region_0 18 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201
3 SD25 SD region_1 18 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201
4 SD36 SD region_0 4 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101
4 nSD31 nSD region_1 4 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101
5 SD37 SD region_0 4 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101
5 nSD32 nSD region_1 4 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101
6 SD38 SD region_0 4 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201
6 nSD33 nSD region_1 4 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201

1.3 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

2. Data Processing & Analysis

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 716157 cells across 12 samples.

Segmented Cell Count in each Samples
Sample Index Cell Count
SD36 66786
SD24 65619
nSD31 62351
SD25 60739
SD23 60150
nSD3 59389
nSD2 57760
SD37 57573
nSD32 57080
nSD1 56980
nSD33 56422
SD38 55308
Identified Cell Spatial Overview on all Samples

Identified Cell Spatial Overview on all Samples

2.2 Batch Effect & Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.

Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.

Umap of cells and colored by batch

Umap of cells and colored by batch

Umap of cells on each batch

Umap of cells on each batch

Leiden Umap can be dividied to 28 clusters

Leiden Umap can be dividied to 28 clusters

2.3 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)[https://doi.org/10.1016/j.cell.2020.04.007]. Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

MapMyCell Annotation Cell Count (Low resolution class)
class_name count
31 OPC-Oligo 169068
30 Astro-Epen 113865
33 Vascular 81284
01 IT-ET Glut 79579
09 CNU-LGE GABA 46159
02 NP-CT-L6b Glut 26207
19 MB Glut 23718
20 MB GABA 23571
34 Immune 20203
12 HY GABA 17974
18 TH Glut 16274
27 MY GABA 13056
11 CNU-HYa GABA 12035
10 LSX GABA 9670
07 CTX-MGE GABA 8602
14 HY Glut 8373
23 P Glut 7881
26 P GABA 6356
24 MY Glut 5320
06 CTX-CGE GABA 5004
08 CNU-MGE GABA 4798
05 OB-IMN GABA 4383
13 CNU-HYa Glut 3076
32 OEC 2747
04 DG-IMN Glut 1605
21 MB Dopa 1574
28 CB GABA 1077
03 OB-CR Glut 625
29 CB Glut 546
17 MH-LH Glut 526
22 MB-HB Sero 521
16 HY MM Glut 374
25 Pineal Glut 60
15 HY Gnrh1 Glut 46
MapMyCell Annotation Cell Count (High resolution subclass)
subclass_name count
7 327 Oligo NN 156007
3 333 Endo NN 51642
0 319 Astro-TE NN 43280
11 318 Astro-NT NN 43234
183 062 STR D2 Gaba 19132
12 334 Microglia NN 17833
32 030 L6 CT CTX Glut 17469
191 061 STR D1 Gaba 16301
25 006 L4/5 IT CTX Glut 15135
8 331 Peri NN 14519
5 321 Astroependymal NN 14279
2 326 OPC NN 13061
219 151 TH Prkcd Grin2c Glut 10524
21 004 L6 IT CTX Glut 9408
18 007 L2/3 IT CTX Glut 8921
146 181 IC Tfap2d Maf Glut 8896
33 005 L5 IT CTX Glut 8532
51 010 IT AON-TT-DP Glut 8103
1 330 VLMC NN 7880
19 009 L2/3 IT PIR-ENTl Glut 6938
195 063 STR D1 Sema5a Gaba 6493
130 323 Ependymal NN 5745
9 332 SMC NN 5322
45 022 L5 ET CTX Glut 5088
61 020 L2/3 IT RSP Glut 4969
27 052 Pvalb Gaba 4877
47 285 MY Lhx1 Gly-Gaba 4526
44 016 CA1-ProS Glut 4382
60 101 ZI Pax6 Gaba 3958
55 029 L6b CTX Glut 3581
43 325 CHOR NN 3354
31 053 Sst Gaba 3143
41 069 LSX Nkx2-1 Gaba 3131
63 032 L5 NP CTX Glut 3124
79 093 RT-ZI Gnb3 Gaba 2928
10 328 OEC NN 2747
39 017 CA3 Glut 2667
204 060 OT D3 Folh1 Gaba 2455
180 235 PG-TRN-LRN Fat2 Glut 2389
70 198 IC Six3 En2 Gaba 2374
131 202 PRT Tcf7l2 Gaba 2342
34 070 LSX Prdm12 Slit2 Gaba 2278
77 098 AHN-SBPV-PVHd Pdrm12 Gaba 2219
22 046 Vip Gaba 2215
30 071 LSX Prdm12 Zeb2 Gaba 2210
108 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba 2150
225 148 AV Col27a1 Glut 2027
73 320 Astro-OLF NN 1997
205 154 PF Fzd5 Glut 1973
4 329 ABC NN 1921
135 207 SCs Dmbx1 Gaba 1838
53 201 PAG-RN Nkx2-2 Otx1 Gaba 1803
54 041 OB-in Frmd7 Gaba 1791
141 205 SC-PAG Lef1 Emx2 Gaba 1787
260 129 VMH Nr5a1 Glut 1780
119 057 NDB-SI-MA-STRv Lhx8 Gaba 1743
167 243 PGRN-PARN-MDRN Hoxb5 Glut 1704
87 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba 1697
6 049 Lamp5 Gaba 1647
271 104 TU-ARH Otp Six6 Gaba 1616
273 215 SNc-VTA-RAmb Foxa1 Dopa 1574
188 037 DG Glut 1571
109 064 STR-PAL Chst9 Gaba 1421
236 134 PH-ant-LHA Otp Bsx Glut 1352
148 222 PB Evx2 Glut 1346
138 213 SCsg Gabrr2 Gaba 1344
83 304 NTS-PARN Neurod2 Gly-Gaba 1304
35 338 Lymphoid NN 1303
78 195 SNr-VTA Pax5 Npas1 Gaba 1286
74 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba 1251
152 090 BST-MPN Six3 Nrgn Gaba 1244
13 210 PRT Mecom Gaba 1218
282 102 DMH-LHA Gsx1 Gaba 1183
29 199 PAG-MRN-RN Foxa2 Gaba 1170
106 209 SCs Pax7 Nfia Gaba 1124
100 089 PVR Six3 Sox3 Gaba 1073
222 107 DMH Hmx2 Gaba 1066
192 081 ACB-BST-FS D1 Gaba 1054
264 086 MPO-ADP Lhx8 Gaba 1038
196 088 BST Tac2 Gaba 1012
215 106 PVpo-VMPO-MPN Hmx2 Gaba 1001
143 068 LSX Otx2 Gaba 998
142 073 MEA-BST Sox6 Gaba 996
229 217 PB Lmx1a Glut 996
209 182 CUN-PPN Evx2 Meis2 Glut 991
75 200 PAG-ND-PCG Onecut1 Gaba 987
48 045 OB-STR-CTX Inh IMN 969
137 187 SCsg Pde5a Glut 964
71 322 Tanycyte NN 952
171 176 SCig Foxb1 Glut 952
95 002 IT EP-CLA Glut 923
24 047 Sncg Gaba 918
103 056 Sst Chodl Gaba 908
92 264 PRNc Otp Gly-Gaba 902
147 119 SI-MA-LPO-LHA Skor1 Glut 890
80 317 Astro-CB NN 885
57 251 NTS Dbh Glut 872
144 085 SI-MPO-LPO Lhx8 Gaba 868
139 208 SC Lef1 Otx2 Gaba 857
90 076 MEA-BST Lhx6 Nfib Gaba 853
217 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut 852
155 177 SCig-an-PPT Foxb1 Glut 848
216 100 AHN Onecut3 Gaba 839
67 033 NP SUB Glut 828
111 054 STR Prox1 Lhx6 Gaba 827
169 180 SCiw Pitx2 Glut 826
227 224 PCG-PRNr Vsx2 Nkx6-1 Glut 826
226 164 APN C1ql4 Glut 817
102 039 OB Meis2 Thsd7b Gaba 782
125 147 AD Serpinb7 Glut 776
207 173 PAG Pou4f2 Glut 771
115 025 CA2-FC-IG Glut 752
133 212 SCs Lef1 Gli3 Gaba 749
93 221 LDT-PCG Vsx2 Lhx4 Glut 748
82 267 CS-PRNr-PCG Tmem163 Otp Gaba 742
117 103 PVHd-DMH Lhx6 Gaba 738
89 021 L4 RSP-ACA Glut 731
281 074 MEA-BST Lhx6 Sp9 Gaba 725
157 172 PAG Pou4f1 Ebf2 Glut 721
193 058 PAL-STR Gaba-Chol 721
15 337 DC NN 705
250 132 AHN-RCH-LHA Otp Fezf1 Glut 702
194 079 CEA-BST Six3 Cyp26b1 Gaba 695
182 278 NLL Gata3 Gly-Gaba 665
159 162 CUN Evx2 Lhx2 Glut 661
94 072 LSX Sall3 Lmo1 Gaba 658
249 108 ARH-PVp Tbx3 Gaba 651
50 283 PRP Otp Gly-Gaba 637
105 196 PAG-PPN Pax5 Sox21 Gaba 634
97 265 PB Sst Gly-Gaba 634
267 082 CEA-BST Ebf1 Pdyn Gaba 613
198 055 STR Lhx8 Gaba 599
23 192 PPN-CUN-PCG Otp En1 Gaba 594
85 270 LDT-DTN Gata3 Nfix Gaba 592
76 023 SUB-ProS Glut 587
96 027 L6b EPd Glut 579
165 238 NTS Phox2b Glut 575
37 305 SPVI-SPVC Sall3 Nfib Gly-Gaba 553
311 128 VMH Fezf1 Glut 549
224 163 APN C1ql2 Glut 545
223 150 CM-IAD-CL-PCN Sema5b Glut 541
181 175 SC Bnc2 Glut 534
52 277 DTN-LDT-IPN Otp Pax3 Gaba 532
154 169 PAG-SC Pou4f1 Zic1 Glut 530
235 216 MB-MY Tph2 Glut-Sero 521
49 003 L5/6 IT TPE-ENT Glut 519
201 161 PAG Pou4f3 Glut 510
28 019 L2/3 IT PPP Glut 493
239 080 CEA-AAA-BST Six3 Sp9 Gaba 488
261 124 MPN-MPO-PVpo Hmx2 Glut 482
160 174 PAG Pou4f2 Mesi2 Glut 481
203 268 CS-PRNr-DR En1 Sox2 Gaba 480
248 133 PVH-SO-PVa Otp Glut 473
240 094 SCH Six6 Cdc14a Gaba 463
149 146 LH Pou4f1 Sox1 Glut 448
121 035 OB Eomes Ms4a15 Glut 423
156 170 PAG-MRN Tfap2b Glut 421
258 311 CBX MLI Megf11 Gaba 415
14 042 OB-out Frmd7 Gaba 412
128 197 SNr Six3 Gaba 404
36 028 L6b/CT ENT Glut 402
158 171 PAG Pou4f1 Bnc2 Glut 399
202 067 LSX Sall3 Pax6 Gaba 395
136 211 SC Tnnt1 Gli3 Gaba 383
134 139 PH-LHA Foxb1 Glut 379
212 166 MRN Pou3f1 C1ql4 Glut 376
161 167 PRC-PAG Tcf7l2 Irx2 Glut 376
305 136 PMv-TMv Pitx2 Glut 373
17 263 CS-RPO Meis2 Gaba 364
283 135 STN-PSTN Pitx2 Glut 361
173 206 SCm-PAG Cdh23 Gaba 357
151 083 CEA-BST Rai14 Pdyn Crh Gaba 353
62 194 MRN-VTN-PPN Pax5 Cdh23 Gaba 353
20 018 L2 IT PPP-APr Glut 352
163 160 PAG-SC Neurod2 Meis2 Glut 351
279 111 TRS-BAC Sln Glut 344
16 271 NI-RPO Gata3 Nr4a2 Gaba 342
72 299 MARN-PPY Ngfr Gly-Gaba 340
213 193 MRN-PPN-CUN Pax8 Gaba 334
295 117 LHA Barhl2 Glut 334
132 066 NDB-SI-ant Prdm12 Gaba 329
140 246 CU-ECU-SPVI Foxb1 Glut 323
127 254 VCO Mafa Meis2 Glut 322
247 141 PH-SUM Foxa1 Glut 321
244 110 BST-po Iigp1 Glut 319
208 144 MM Foxb1 Glut 318
107 051 Pvalb chandelier Gaba 308
164 245 SPVI-SPVC Tlx3 Ebf3 Glut 305
65 272 LDT-PCG-CS Gata3 Lhx1 Gaba 303
129 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba 302
175 188 SCop Sln Glut 299
56 314 CB Granule Glut 288
231 165 PAG-MRN Pou3f1 Glut 286
200 092 TMv-PMv Tbx3 Hist-Gaba 285
189 013 COAp Grxcr2 Glut 280
199 126 ARH-PVp Tbx3 Glut 279
179 140 PMd-LHA Foxb1 Glut 278
296 097 PVHd-SBPV Six3 Prox1 Gaba 278
26 050 Lamp5 Lhx6 Gaba 274
110 012 MEA Slc17a7 Glut 271
58 229 PB-NTS Phox2b Ebf3 Lmx1b Glut 267
252 115 MS-SF Bsx Glut 266
116 335 BAM NN 260
101 315 DCO UBC Glut 258
104 044 OB Dopa-Gaba 251
170 220 PB Pax5 Glut 248
303 125 DMH Hmx2 Glut 247
302 127 DMH-LHA Vgll2 Glut 242
277 155 PRC-PAG Pax6 Glut 241
185 099 SBPV-PVa Six6 Satb2 Gaba 240
245 152 RE-Xi Nox4 Glut 238
99 313 CBX Purkinje Gaba 235
293 131 LHA-AHN-PVH Otp Trh Glut 233
232 287 MV-SPIV-PRP Dmbx1 Gly-Gaba 231
290 118 ADP-MPO Trp73 Glut 229
123 048 RHP-COA Ndnf Gaba 224
176 105 TMd-DMH Foxd2 Gaba 222
162 237 PRP-NI-PRNc-GRN Otp Glut 215
197 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut 210
174 279 PSV Pax2 Gly-Gaba 205
187 114 COAa-PAA-MEA Barhl2 Glut 205
120 290 MY Prox1 Lmo7 Gly-Gaba 204
126 036 HPF CR Glut 202
177 261 HB Calcb Chol 197
238 109 LGv-ZI Otx2 Gaba 196
145 257 SPVC Ccdc172 Glut 191
246 156 MB-ant-ve Dmrta2 Glut 189
42 293 PAS-MV Ebf2 Gly-Gaba 188
59 308 DCO Il22 Gly-Gaba 186
270 231 IPN-LDT Vsx2 Nkx6-1 Glut 186
114 059 GPe-SI Sox6 Cyp26b1 Gaba 180
269 248 MV-SPIV Zic4 Neurod2 Glut 180
46 065 IA Mgp Gaba 177
287 223 B-PB Nr4a2 Glut 172
86 214 IPN Otp Crisp1 Gaba 166
298 276 LDT-PCG St18 Gaba 163
327 292 MV Nkx6-1 Gly-Gaba 163
40 008 L2/3 IT ENT Glut 159
166 149 PVT-PT Ntrk1 Glut 150
68 204 SC Otx2 Gcnt4 Gaba 146
309 116 AVPV-MEPO-SFO Tbr1 Glut 139
64 273 PDTg-PCG Pax6 Gaba 135
172 186 SCop Pou4f2 Neurod2 Glut 133
153 303 IRN Dmbx1 Pax2 Gly-Gaba 133
186 228 PSV Pvalb Lhx2 Glut 129
297 130 LHA Pmch Glut 124
168 178 SCig Foxb1 Otx2 Glut 124
285 294 MV Pax6 Gly-Gaba 123
118 034 NP PPP Glut 123
88 043 OB-mi Frmd7 Gaba 119
286 282 POR Spp1 Gly-Gaba 117
265 288 MDRN Hoxb5 Ebf2 Gly-Gaba 116
254 179 SCdg-PAG Tfap2b Glut 113
259 316 Bergmann NN 113
278 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba 113
292 084 BST-SI-AAA Six3 Slc22a3 Gaba 113
221 113 MEA-COA-BMA Ccdc42 Glut 111
230 298 PRP Gata3 Slc6a5 Gly-Gaba 111
210 309 CB PLI Gly-Gaba 111
294 121 MEA-BST Otp Zic2 Glut 110
184 296 RPA Pax6 Hoxb5 Gly-Gaba 107
228 233 NLL-SOC Spp1 Glut 106
178 185 SCig Tfap2b Chrnb3 Glut 103
262 159 IF-RL-CLI-PAG Foxa1 Glut 103
66 336 Monocytes NN 102
313 312 CBX MLI Cdh22 Gaba 101
220 226 PRNc-PARN Tlx1 Glut 101
69 031 CT SUB Glut 101
38 014 LA-BLA-BMA-PA Glut 101
84 011 L2 IT ENT-po Glut 100
214 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut 100
251 078 SI-MA-ACB Ebf1 Bnc2 Gaba 99
233 234 MEV Ppp1r1c Glut 96
112 075 MEA-BST Lhx6 Nr2e1 Gaba 94
256 138 PH Pitx2 Glut 94
234 286 PPY-PGRNl Vip Glyc-Gaba 88
268 077 CEA-BST Gal Avp Gaba 86
206 157 RN Spp1 Glut 80
315 145 MH Tac2 Glut 78
81 001 CLA-EPd-CTX Car3 Glut 75
211 123 DMH Nkx2-4 Glut 74
314 297 CU-ECU Pax2 Gly-Gaba 73
263 281 POR Gata3 Gly-Gaba 71
237 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba 71
266 191 PAG-MRN Rln3 Gaba 70
317 232 LDT Vsx2 Nkx6-1 Nfib Glut 68
253 256 SPVC Mafa Glut 67
310 252 DMX VII Tbx20 Chol 66
308 122 LHA-MEA Otp Glut 66
190 015 ENTmv-PA-COAp Glut 62
113 302 MV Xdh Gly-Gaba 62
243 262 Pineal Crx Glut 60
98 040 OB Trdn Gaba 59
306 143 MM-ant Foxb1 Glut 56
307 230 PRNr Otp Nfib Glut 54
257 158 MRN-PAG Nkx6-1 Glut 54
280 091 ARH-PVi Six6 Dopa-Gaba 47
324 269 LDT Fgf7 Gaba 47
291 142 HY Gnrh1 Glut 46
150 153 MG-POL-SGN Nts Glut 45
218 190 ND-INC Foxd2 Glut 43
241 275 PDTg Otp Olig3 Gaba 41
274 250 CBN Neurod2 Pvalb Glut 39
334 253 IO Fgl2 Glut 38
332 112 GPi Tbr1 Cngb3 Gaba-Glut 36
242 038 DG-PIR Ex IMN 34
320 096 PVHd Gsc Gaba 33
316 244 MV-SPIV Slc6a2 Glut 32
322 137 PH-an Pitx2 Glut 30
304 310 CBX Golgi Gly-Gaba 29
301 184 PAG Tcf24 Glut 28
300 120 MEA Otp Foxp2 Glut 27
124 307 RO-RPA Pkd2l1 Gaba 26
319 324 Hypendymal NN 26
288 026 NLOT Rho Glut 24
299 218 PSV Lmx1a Trpv6 Glut 20
276 255 SPVO Mafa Meis2 Glut 20
275 295 CBN Dmbx1 Gaba 20
328 239 MARN-GRN Pyy Glut 19
330 236 IRN Vip Glut 15
272 258 SPVC Nmu Glut 13
255 289 MDRNd Prox1 Pax6 Gly-Gaba 13
323 242 PGRNd Dmbx1 Glut 12
325 274 PDTg Otp Shroom3 Gaba 12
289 095 DMH Prdm13 Gaba 11
318 227 PB-PSV Phox2b Glut 8
333 266 PRNc Prox1 Brs3 Gly-Gaba 7
312 301 MV Nr4a2 Gly-Gaba 7
91 024 L5 PPP Glut 7
284 219 PB-SUT Tlx3 Lhx2 Glut 7
331 240 MDRNv Lhx4 Qrfprl Glut 7
329 249 NTS Aldh1a2 Glut 6
326 189 PAG Ucn Glut 3
122 280 NLL-po Pax7 Gaba 2
321 260 MDRNv Crp Glut 2
335 183 PBG Mtnr1a Glut-Chol 1

2.3.1 Spatial cell type (Neurons)

2.3.2 Spatial cell type (Non-Neurons)

3. Gene differentiation

3.2 18 month (SD v.s. nSD)

Here, we use Wilcoxon rank-sum to compute differential expression. The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Rph3a 28.944470 1.388900 0.0000000 0.0000000
1 Plxna1 28.046041 2.301442 0.0000000 0.0000000
2 Agt 27.943491 -2.393148 0.0000000 0.0000000
3 Src 27.921728 4.487398 0.0000000 0.0000000
4 Cbs 26.396925 -1.071521 0.0000000 0.0000000
7 Celsr1 23.590359 -2.000866 0.0000000 0.0000000
8 Ppp1r3g 23.220676 -1.323350 0.0000000 0.0000000
10 Aldh1l1 22.330301 -1.132953 0.0000000 0.0000000
55 Selplg 16.221874 1.753074 0.0000000 0.0000000
60 Adgra1 15.440236 1.416462 0.0000000 0.0000000
61 Gfap 15.413177 -2.036321 0.0000000 0.0000000
67 Sorl1 14.438042 -1.571411 0.0000000 0.0000000
70 Gria1 13.162408 2.263560 0.0000000 0.0000000
73 Lmna 12.090912 2.315438 0.0000000 0.0000000
75 Bsg 11.607372 -1.092800 0.0000000 0.0000000
76 Cpne6 11.167419 1.045617 0.0000000 0.0000000
80 Sox10 8.650637 -6.846686 0.0000000 0.0000000
81 Nptxr 8.103887 3.055979 0.0000000 0.0000000
87 Csf1 5.623299 -1.808446 0.0000000 0.0000000
88 Psen2 5.352371 -2.142666 0.0000001 0.0000001
90 Kcnh2 4.505847 1.523469 0.0000066 0.0000073
96 C4b 2.913784 -6.554722 0.0035708 0.0037746
98 Epha10 2.211155 1.781221 0.0270251 0.0282099
119 Grm2 -2.206856 1.420873 0.0273241 0.0284626
126 Calb2 -3.318561 3.206868 0.0009048 0.0009646
137 Htr5a -4.398849 1.760891 0.0000109 0.0000120
143 Tshz2 -5.829703 -2.443032 0.0000000 0.0000000
146 Tcerg1l -6.662591 1.176542 0.0000000 0.0000000
155 Adgrl2 -7.608365 -2.702438 0.0000000 0.0000000
162 Sstr3 -8.797502 1.657975 0.0000000 0.0000000
176 Arc -10.425211 -1.692957 0.0000000 0.0000000
180 Nrg1 -10.680949 -2.005716 0.0000000 0.0000000
184 Nefm -11.140943 -1.066463 0.0000000 0.0000000
186 Dlx2 -11.257780 3.168033 0.0000000 0.0000000
188 Elfn1 -11.407543 2.939911 0.0000000 0.0000000
195 Cxcl2 -12.265088 3.121446 0.0000000 0.0000000
200 Ppp1r1b -12.857080 -2.595633 0.0000000 0.0000000
209 Fibcd1 -13.702404 5.657442 0.0000000 0.0000000
211 Tpbg -13.738964 -1.768342 0.0000000 0.0000000
217 Ngb -14.125284 -2.728884 0.0000000 0.0000000
218 Fezf2 -14.184770 1.452152 0.0000000 0.0000000
223 Rspo2 -14.398157 1.309919 0.0000000 0.0000000
236 Gad2 -15.339884 -1.255430 0.0000000 0.0000000
238 Mmp9 -15.384572 4.504550 0.0000000 0.0000000
239 Ube3a -15.408014 1.504243 0.0000000 0.0000000
241 Cck -15.426351 -3.211665 0.0000000 0.0000000
244 Grp -15.597065 -5.945525 0.0000000 0.0000000
248 Lratd2 -15.680084 -1.022045 0.0000000 0.0000000
249 Plch1 -15.724257 1.516138 0.0000000 0.0000000
250 Snca -15.827183 2.480958 0.0000000 0.0000000
252 Sst -16.046322 4.112230 0.0000000 0.0000000
255 Pomc -16.167488 -1.276712 0.0000000 0.0000000
259 Gad1 -16.534620 1.037472 0.0000000 0.0000000
266 Pdlim1 -16.808880 -1.300291 0.0000000 0.0000000
271 Sctr -17.205660 -2.566417 0.0000000 0.0000000
273 Oxtr -17.342897 2.116546 0.0000000 0.0000000
286 Gpr15 -17.965555 -2.747449 0.0000000 0.0000000
288 Etv1 -18.038576 -1.116177 0.0000000 0.0000000
289 Pde6g -18.107447 1.072131 0.0000000 0.0000000
290 Gm2115 -18.110088 1.615371 0.0000000 0.0000000
294 Foxp2 -18.276554 -3.319793 0.0000000 0.0000000
296 Clic6 -18.390594 1.402710 0.0000000 0.0000000
297 Cplx3 -18.580791 6.148846 0.0000000 0.0000000
305 Ngf -18.827608 1.300512 0.0000000 0.0000000
315 Egr1 -19.122837 -1.319314 0.0000000 0.0000000
326 Tacr3 -19.397455 -2.967331 0.0000000 0.0000000
342 Epha7 -19.869835 4.404749 0.0000000 0.0000000
348 Sla2 -20.030058 1.551933 0.0000000 0.0000000
352 Nr4a2 -20.126863 -1.113119 0.0000000 0.0000000
369 Fos -20.664042 -1.216638 0.0000000 0.0000000
371 Acan -20.700275 1.322526 0.0000000 0.0000000
379 Sncg -20.835150 -1.271624 0.0000000 0.0000000
381 Rbp4 -20.856358 -1.204773 0.0000000 0.0000000
384 Smad3 -20.894398 2.588649 0.0000000 0.0000000
390 Iyd -21.058645 -2.184489 0.0000000 0.0000000
393 Clec7a -21.123037 -1.328190 0.0000000 0.0000000
401 Cxcl10 -21.363434 1.038642 0.0000000 0.0000000
402 Bcl11b -21.374462 1.699636 0.0000000 0.0000000
410 Cox6a2 -21.546738 -1.886645 0.0000000 0.0000000
412 Mas1 -21.571447 1.338628 0.0000000 0.0000000
414 Il10 -21.614138 1.400637 0.0000000 0.0000000
420 Mrc1 -21.791927 1.297373 0.0000000 0.0000000
425 Pvalb -21.873800 1.053480 0.0000000 0.0000000
429 Chodl -22.032022 1.236844 0.0000000 0.0000000
438 Scgb3a1 -22.204580 -6.913044 0.0000000 0.0000000
441 Ros1 -22.237371 3.902720 0.0000000 0.0000000
447 Batf3 -22.475718 2.185340 0.0000000 0.0000000
455 Lcn2 -22.670600 1.382140 0.0000000 0.0000000
457 Crh -22.687916 1.723271 0.0000000 0.0000000
462 Fev -22.875030 -2.395585 0.0000000 0.0000000
467 Homer1 -23.125505 4.137401 0.0000000 0.0000000
468 Ms4a7 -23.191578 2.800186 0.0000000 0.0000000
470 Glp2r -23.239897 2.384667 0.0000000 0.0000000
474 Vipr2 -23.543062 1.493215 0.0000000 0.0000000
475 Tac1 -23.641481 1.221806 0.0000000 0.0000000
479 Meis2 -24.170412 1.223973 0.0000000 0.0000000
487 Cdh9 -25.646890 1.549408 0.0000000 0.0000000
489 Col6a1 -26.107733 -1.523172 0.0000000 0.0000000
491 Igfbp6 -26.176900 2.712716 0.0000000 0.0000000
495 Scn4b -27.879620 -2.264821 0.0000000 0.0000000
496 Fosb -29.593323 -3.072714 0.0000000 0.0000000
497 Slc29a1 -30.019459 1.307068 0.0000000 0.0000000

3.3 4 month (SD v.s. nSD)

Here, we use Wilcoxon rank-sum to compute differential expression. The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Meis2 19.857416 1.860012 0.0000000 0.0000000
1 Bcl6 18.995796 1.759851 0.0000000 0.0000000
4 Bcl11b 14.835252 2.319346 0.0000000 0.0000000
5 Col6a1 14.528924 -1.192809 0.0000000 0.0000000
6 Smad3 14.467199 1.739373 0.0000000 0.0000000
15 Cdh9 11.597134 1.728570 0.0000000 0.0000000
16 Tac1 11.501706 1.551762 0.0000000 0.0000000
20 Scn4b 10.846497 -1.051456 0.0000000 0.0000000
36 Ppp1r1b 8.781802 -1.500966 0.0000000 0.0000000
37 Spp1 8.592707 1.323700 0.0000000 0.0000000
38 Gria3 8.470551 11.563471 0.0000000 0.0000000
41 Gm2115 8.273608 2.770439 0.0000000 0.0000000
42 Slc2a4 8.209332 1.470614 0.0000000 0.0000000
53 Pdlim1 7.537143 4.285157 0.0000000 0.0000000
66 Rspo1 6.678997 -1.490347 0.0000000 0.0000000
67 Pf4 6.647812 -2.367006 0.0000000 0.0000000
69 Xdh 6.560428 2.153479 0.0000000 0.0000000
75 Lcn2 6.301711 5.069178 0.0000000 0.0000000
81 Gm11627 6.055383 1.426082 0.0000000 0.0000000
84 Batf3 5.873402 1.285753 0.0000000 0.0000000
90 Igf1 5.631518 2.873254 0.0000000 0.0000001
91 Chat 5.607643 -2.370454 0.0000000 0.0000001
93 Ido1 5.469242 -1.877326 0.0000000 0.0000001
97 Pde11a 5.376929 -1.174282 0.0000001 0.0000002
100 Ly6c1 5.322024 1.063759 0.0000001 0.0000003
112 Ms4a7 5.110157 2.833157 0.0000003 0.0000009
116 Homer1 4.918252 1.390868 0.0000009 0.0000024
118 Oxtr 4.893650 -1.570102 0.0000010 0.0000027
123 Htr3a 4.789054 -2.861219 0.0000017 0.0000044
124 Lpl 4.767579 1.893277 0.0000019 0.0000049
125 Dapl1 4.753054 1.184902 0.0000020 0.0000052
130 Syt17 4.663308 6.665681 0.0000031 0.0000078
139 Taar9 4.588082 -1.076370 0.0000045 0.0000108
146 Tshr 4.393799 1.294549 0.0000111 0.0000259
154 Sst 4.312500 2.224645 0.0000161 0.0000357
156 Smim40 4.248860 1.927524 0.0000215 0.0000469
158 Cd74 4.182188 -1.046423 0.0000289 0.0000622
162 Gbx2 4.074254 1.855168 0.0000462 0.0000974
169 Ccr6 3.939631 -7.022958 0.0000816 0.0001636
181 Ms4a4a 3.798194 -2.100815 0.0001458 0.0002760
184 Ace 3.749998 -1.285993 0.0001768 0.0003312
187 Tacr2 3.696152 2.475232 0.0002189 0.0004054
190 Ccl4 3.645473 -1.182006 0.0002669 0.0004870
196 Nxph4 3.470788 4.181598 0.0005189 0.0009234
209 Cnr1 3.220196 -3.259706 0.0012810 0.0021494
213 Lhx6 3.143489 1.135690 0.0016695 0.0027458
225 Neurod6 2.925323 -1.642305 0.0034410 0.0053598
229 Cox6a2 2.856265 1.809596 0.0042866 0.0065544
232 Rbp4 2.789104 4.962527 0.0052854 0.0079361
236 Pilra 2.774602 -3.206640 0.0055269 0.0082002
252 Ntf3 2.351158 -1.618051 0.0187151 0.0255594
255 C3 2.346703 1.114059 0.0189404 0.0256644
256 Elfn1 2.321497 3.655799 0.0202600 0.0273784
258 Cxcl10 2.282540 1.158835 0.0224575 0.0301039
260 Ngb 2.189410 -2.272303 0.0285671 0.0378874
385 Grm1 -2.233356 -1.942039 0.0255255 0.0340340
386 Cckbr -2.317601 1.219366 0.0204710 0.0275889
406 Kcnh2 -3.015115 1.002094 0.0025688 0.0040775
411 Psen2 -3.201180 -1.239283 0.0013687 0.0022735
413 Fam131a -3.354972 3.037981 0.0007937 0.0013780
414 Crhr1 -3.380944 2.165697 0.0007224 0.0012585
416 Fezf2 -3.612585 5.244341 0.0003032 0.0005472
431 Itga7 -4.391043 -1.292447 0.0000113 0.0000261
436 Tshz2 -5.214677 -1.961273 0.0000002 0.0000005
439 Celsr1 -5.325972 -1.813416 0.0000001 0.0000003
441 Lmna -5.425329 1.126918 0.0000001 0.0000002
448 Tcerg1l -6.026394 3.578800 0.0000000 0.0000000
455 Arc -7.110542 3.051091 0.0000000 0.0000000
456 C4b -7.187853 2.030230 0.0000000 0.0000000
460 Nrg2 -7.565744 2.135639 0.0000000 0.0000000
463 Dkk3 -8.174537 2.894435 0.0000000 0.0000000
467 Grm2 -8.460107 4.292875 0.0000000 0.0000000
469 Syngap1 -8.839329 1.376613 0.0000000 0.0000000
471 Cars -9.514578 -1.211363 0.0000000 0.0000000
473 Adrb1 -9.677060 -3.604486 0.0000000 0.0000000
478 Bsg -10.832339 -1.107190 0.0000000 0.0000000
482 Nrg3 -11.437200 1.925336 0.0000000 0.0000000
484 Kcnc1 -11.554249 1.425769 0.0000000 0.0000000
485 Src -11.652369 1.138358 0.0000000 0.0000000
489 Nr4a1 -13.221887 1.547676 0.0000000 0.0000000
490 Egr1 -13.570163 3.308445 0.0000000 0.0000000
491 Tcf7l2 -13.713945 -1.873934 0.0000000 0.0000000
494 Sorl1 -15.240706 -1.820602 0.0000000 0.0000000
497 Fos -17.436176 3.403238 0.0000000 0.0000000
499 Rph3a -25.370182 1.157358 0.0000000 0.0000000

3.4.1 18 month, HY (Hypothalamus) Gaba, SD v.s. nSD

Here, we use Wilcoxon rank-sum to compute differential expression. The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Gria1 13.910446 1.050308 0.0000000 0.0000000
1 Bin1 10.811795 1.134469 0.0000000 0.0000000
43 Camk2g 6.785084 1.594544 0.0000000 0.0000000
65 Camk2a 5.819418 2.834248 0.0000000 0.0000000
70 Sorl1 5.413987 -2.118668 0.0000001 0.0000001
87 Ngrn 3.204597 1.503384 0.0013525 0.0016991
98 Camk4 2.360472 -1.713056 0.0182517 0.0213221
175 Clic6 -2.629364 6.169227 0.0085545 0.0102082
188 Cacng5 -3.178469 1.244893 0.0014806 0.0018507
192 Penk -3.355078 -2.878961 0.0007934 0.0010043
213 Lhx6 -4.433422 1.321839 0.0000093 0.0000127
215 Tnf -4.473998 -1.064348 0.0000077 0.0000106
219 Map4k3 -4.561144 1.280793 0.0000051 0.0000071
242 Crhbp -5.199602 1.343332 0.0000002 0.0000003
250 Rorb -5.564923 -2.121769 0.0000000 0.0000000
255 Bmp2 -5.693881 5.277444 0.0000000 0.0000000
263 Cdh12 -5.959627 1.127013 0.0000000 0.0000000
264 Ctsl -5.961489 2.126253 0.0000000 0.0000000
271 Htr2c -6.053985 3.211407 0.0000000 0.0000000
272 Pdyn -6.059630 1.900159 0.0000000 0.0000000
276 Crhr1 -6.102454 -1.718627 0.0000000 0.0000000
289 Slc29a1 -6.555049 -1.712681 0.0000000 0.0000000
294 Ndst4 -6.626977 -4.176397 0.0000000 0.0000000
307 Il10 -6.883614 1.055847 0.0000000 0.0000000
321 Iyd -7.003740 -1.973775 0.0000000 0.0000000
329 Atf3 -7.081428 1.241385 0.0000000 0.0000000
333 Cplx3 -7.104630 -1.097364 0.0000000 0.0000000
335 Ccl4 -7.117582 -2.427280 0.0000000 0.0000000
336 Gng8 -7.123683 -2.386154 0.0000000 0.0000000
353 Fos -7.269758 -5.033966 0.0000000 0.0000000
358 Cst7 -7.322256 -2.546356 0.0000000 0.0000000
366 Lpl -7.407818 2.910695 0.0000000 0.0000000
371 Chrna5 -7.454066 1.146197 0.0000000 0.0000000
374 Lcn2 -7.459715 1.972724 0.0000000 0.0000000
393 Bdkrb1 -7.557772 2.057314 0.0000000 0.0000000
395 Smim40 -7.571732 1.078624 0.0000000 0.0000000
398 Epha7 -7.592292 1.180845 0.0000000 0.0000000
403 Tnnt3 -7.630213 -2.169084 0.0000000 0.0000000
410 Fosl2 -7.680527 1.093957 0.0000000 0.0000000
411 Igf1 -7.683569 1.619427 0.0000000 0.0000000
418 Crh -7.732072 -2.088553 0.0000000 0.0000000
419 Calb1 -7.745038 5.481071 0.0000000 0.0000000
420 Cxcl10 -7.756198 1.090602 0.0000000 0.0000000
424 Pilra -7.771607 1.853035 0.0000000 0.0000000
427 Lgals3 -7.805723 1.070453 0.0000000 0.0000000
433 Opn3 -7.854511 -1.495114 0.0000000 0.0000000
445 Dapl1 -7.940217 1.245576 0.0000000 0.0000000
448 Gpr34 -7.953693 1.456309 0.0000000 0.0000000
449 Mki67 -7.961286 -1.356052 0.0000000 0.0000000
459 Mrc1 -8.068907 -2.957619 0.0000000 0.0000000
461 Vipr2 -8.087303 -1.824283 0.0000000 0.0000000
466 Enpp6 -8.194320 1.872020 0.0000000 0.0000000
471 Clec7a -8.295661 -1.907428 0.0000000 0.0000000
472 Fev -8.320689 -3.552570 0.0000000 0.0000000
476 Myh8 -8.376872 4.291716 0.0000000 0.0000000
478 Klk6 -8.418024 1.107549 0.0000000 0.0000000
479 Slc6a3 -8.463105 1.908241 0.0000000 0.0000000
480 C3 -8.474239 1.487186 0.0000000 0.0000000
482 Mme -8.534939 1.429534 0.0000000 0.0000000
485 Chrna6 -8.592888 1.907402 0.0000000 0.0000000
487 Cp -8.709121 1.056720 0.0000000 0.0000000
488 Adgrg7 -8.711240 -3.050283 0.0000000 0.0000000
490 Sla -8.778913 1.293025 0.0000000 0.0000000
491 Tlr4 -8.880650 3.578067 0.0000000 0.0000000
492 Fosb -8.922410 1.561501 0.0000000 0.0000000
493 Cxcl2 -8.933720 2.635271 0.0000000 0.0000000
494 Ramp3 -9.050678 -2.652708 0.0000000 0.0000000
495 Pvalb -9.421059 -1.210859 0.0000000 0.0000000
497 Adamts15 -9.691435 -1.427218 0.0000000 0.0000000
498 Pthlh -11.643683 -1.849253 0.0000000 0.0000000

3.4.2 4 month, HY (Hypothalamus) Gaba, SD v.s. nSD

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Gria1 13.910446 1.050308 0.0000000 0.0000000
1 Bin1 10.811795 1.134469 0.0000000 0.0000000
43 Camk2g 6.785084 1.594544 0.0000000 0.0000000
65 Camk2a 5.819418 2.834248 0.0000000 0.0000000
70 Sorl1 5.413987 -2.118668 0.0000001 0.0000001
87 Ngrn 3.204597 1.503384 0.0013525 0.0016991
98 Camk4 2.360472 -1.713056 0.0182517 0.0213221
175 Clic6 -2.629364 6.169227 0.0085545 0.0102082
188 Cacng5 -3.178469 1.244893 0.0014806 0.0018507
192 Penk -3.355078 -2.878961 0.0007934 0.0010043
213 Lhx6 -4.433422 1.321839 0.0000093 0.0000127
215 Tnf -4.473998 -1.064348 0.0000077 0.0000106
219 Map4k3 -4.561144 1.280793 0.0000051 0.0000071
242 Crhbp -5.199602 1.343332 0.0000002 0.0000003
250 Rorb -5.564923 -2.121769 0.0000000 0.0000000
255 Bmp2 -5.693881 5.277444 0.0000000 0.0000000
263 Cdh12 -5.959627 1.127013 0.0000000 0.0000000
264 Ctsl -5.961489 2.126253 0.0000000 0.0000000
271 Htr2c -6.053985 3.211407 0.0000000 0.0000000
272 Pdyn -6.059630 1.900159 0.0000000 0.0000000
276 Crhr1 -6.102454 -1.718627 0.0000000 0.0000000
289 Slc29a1 -6.555049 -1.712681 0.0000000 0.0000000
294 Ndst4 -6.626977 -4.176397 0.0000000 0.0000000
307 Il10 -6.883614 1.055847 0.0000000 0.0000000
321 Iyd -7.003740 -1.973775 0.0000000 0.0000000
329 Atf3 -7.081428 1.241385 0.0000000 0.0000000
333 Cplx3 -7.104630 -1.097364 0.0000000 0.0000000
335 Ccl4 -7.117582 -2.427280 0.0000000 0.0000000
336 Gng8 -7.123683 -2.386154 0.0000000 0.0000000
353 Fos -7.269758 -5.033966 0.0000000 0.0000000
358 Cst7 -7.322256 -2.546356 0.0000000 0.0000000
366 Lpl -7.407818 2.910695 0.0000000 0.0000000
371 Chrna5 -7.454066 1.146197 0.0000000 0.0000000
374 Lcn2 -7.459715 1.972724 0.0000000 0.0000000
393 Bdkrb1 -7.557772 2.057314 0.0000000 0.0000000
395 Smim40 -7.571732 1.078624 0.0000000 0.0000000
398 Epha7 -7.592292 1.180845 0.0000000 0.0000000
403 Tnnt3 -7.630213 -2.169084 0.0000000 0.0000000
410 Fosl2 -7.680527 1.093957 0.0000000 0.0000000
411 Igf1 -7.683569 1.619427 0.0000000 0.0000000
418 Crh -7.732072 -2.088553 0.0000000 0.0000000
419 Calb1 -7.745038 5.481071 0.0000000 0.0000000
420 Cxcl10 -7.756198 1.090602 0.0000000 0.0000000
424 Pilra -7.771607 1.853035 0.0000000 0.0000000
427 Lgals3 -7.805723 1.070453 0.0000000 0.0000000
433 Opn3 -7.854511 -1.495114 0.0000000 0.0000000
445 Dapl1 -7.940217 1.245576 0.0000000 0.0000000
448 Gpr34 -7.953693 1.456309 0.0000000 0.0000000
449 Mki67 -7.961286 -1.356052 0.0000000 0.0000000
459 Mrc1 -8.068907 -2.957619 0.0000000 0.0000000
461 Vipr2 -8.087303 -1.824283 0.0000000 0.0000000
466 Enpp6 -8.194320 1.872020 0.0000000 0.0000000
471 Clec7a -8.295661 -1.907428 0.0000000 0.0000000
472 Fev -8.320689 -3.552570 0.0000000 0.0000000
476 Myh8 -8.376872 4.291716 0.0000000 0.0000000
478 Klk6 -8.418024 1.107549 0.0000000 0.0000000
479 Slc6a3 -8.463105 1.908241 0.0000000 0.0000000
480 C3 -8.474239 1.487186 0.0000000 0.0000000
482 Mme -8.534939 1.429534 0.0000000 0.0000000
485 Chrna6 -8.592888 1.907402 0.0000000 0.0000000
487 Cp -8.709121 1.056720 0.0000000 0.0000000
488 Adgrg7 -8.711240 -3.050283 0.0000000 0.0000000
490 Sla -8.778913 1.293025 0.0000000 0.0000000
491 Tlr4 -8.880650 3.578067 0.0000000 0.0000000
492 Fosb -8.922410 1.561501 0.0000000 0.0000000
493 Cxcl2 -8.933720 2.635271 0.0000000 0.0000000
494 Ramp3 -9.050678 -2.652708 0.0000000 0.0000000
495 Pvalb -9.421059 -1.210859 0.0000000 0.0000000
497 Adamts15 -9.691435 -1.427218 0.0000000 0.0000000
498 Pthlh -11.643683 -1.849253 0.0000000 0.0000000

3.4.3 18 month, PIR (piriform cortex) Glut, SD v.s. nSD

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Src 6.302519 1.069231 0.0000000 0.0000001
14 Camk4 3.390334 -1.735682 0.0006981 0.0151755
15 Dbh 3.341551 1.078994 0.0008331 0.0173566
490 Kctd4 -3.124651 -1.021189 0.0017802 0.0287123

3.4.4 4 month, PIR (piriform cortex) Glut, SD v.s. nSD

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
4 Trem2 5.721743 -2.216433 0.0000000 0.0000003
192 Slc29a1 -2.628896 1.467588 0.0085663 0.0113830
193 Pcdhac2 -2.634024 -2.786669 0.0084380 0.0112506
194 Ly6g6e -2.641760 1.593219 0.0082477 0.0110263
202 Pdzrn4 -2.795896 1.767270 0.0051756 0.0070705
207 Mhrt -2.851343 -1.428840 0.0043535 0.0060249
210 Agtr1a -2.938321 -1.887335 0.0033000 0.0046348
211 St8sia4 -2.944761 1.124800 0.0032320 0.0045522
212 P2ry12 -3.002711 -1.528758 0.0026759 0.0037795
214 Vgf -3.042030 2.181501 0.0023499 0.0033379
222 Grp -3.154700 -3.659134 0.0016066 0.0023489
254 Cpne5 -3.481513 -1.712894 0.0004986 0.0008068
265 Kcnq1 -3.689855 -2.651553 0.0002244 0.0003765
266 Mrc1 -3.700234 2.103028 0.0002154 0.0003626
277 Gpr158 -3.829849 -1.509359 0.0001282 0.0002250
282 Camk4 -3.861574 1.763910 0.0001127 0.0002012
301 Tcerg1 -4.020323 1.104653 0.0000581 0.0001113
314 Chrna5 -4.094277 3.003494 0.0000423 0.0000854
316 Kcnab1 -4.105455 2.599829 0.0000404 0.0000820
318 Musk -4.117432 -2.544906 0.0000383 0.0000785
323 Lcn2 -4.156733 -2.535903 0.0000323 0.0000678
325 Htr1a -4.186489 1.322711 0.0000283 0.0000600
327 Apoc1 -4.193675 1.399103 0.0000274 0.0000589
341 Penk -4.308225 -1.340506 0.0000165 0.0000377
350 Clec7a -4.352885 -1.979285 0.0000134 0.0000321
358 Glp2r -4.392133 1.307139 0.0000112 0.0000283
360 Cass4 -4.405920 -1.434173 0.0000105 0.0000269
384 Epha1 -4.606543 1.244339 0.0000041 0.0000123
389 Ccr6 -4.617012 -1.092814 0.0000039 0.0000120
398 Egr2 -4.663765 -1.503979 0.0000031 0.0000102
403 Ms4a7 -4.719603 1.138078 0.0000024 0.0000083
410 Gpr34 -4.755533 -1.519988 0.0000020 0.0000074
415 Nos1 -4.812187 2.463567 0.0000015 0.0000058
432 Coch -4.963573 -1.590729 0.0000007 0.0000032
442 Homer1 -5.015330 1.468630 0.0000005 0.0000028
449 Reln -5.063751 1.922927 0.0000004 0.0000024
460 Pdgfa -5.159725 1.100604 0.0000002 0.0000018
466 Scgb3a1 -5.289375 -7.901140 0.0000001 0.0000011
467 Kcnc1 -5.310649 2.899389 0.0000001 0.0000010
470 Adgrg7 -5.353108 2.008718 0.0000001 0.0000009
472 Gpr63 -5.385455 1.124321 0.0000001 0.0000008
476 Nrg1 -5.443688 2.988994 0.0000001 0.0000007
478 Atf3 -5.496297 -4.110588 0.0000000 0.0000006
480 Lgals3 -5.556996 -4.428739 0.0000000 0.0000005
482 Src -5.595659 -1.051466 0.0000000 0.0000004
489 Lrrc55 -5.862589 -1.163032 0.0000000 0.0000002
490 Folr1 -5.953629 1.781058 0.0000000 0.0000001

3.4.5 18 month, Endothelial Cell, SD v.s. nSD

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
59 Vtn 4.309298 -1.464144 0.0000164 0.0000198
69 Camk2a 2.632321 -1.064659 0.0084804 0.0092580
137 Ngrn -3.783030 4.242140 0.0001549 0.0001818
143 Trib2 -3.989235 -3.335695 0.0000663 0.0000795
153 Pthlh -4.432126 1.939382 0.0000093 0.0000115
181 Vcam1 -5.167849 4.286670 0.0000002 0.0000003
244 Oxtr -6.097137 2.128858 0.0000000 0.0000000
254 Ptpru -6.164821 -1.271227 0.0000000 0.0000000
258 Trhr -6.185821 -1.492926 0.0000000 0.0000000
299 Taar9 -6.432091 -2.767483 0.0000000 0.0000000
309 Il1b -6.460995 -1.475755 0.0000000 0.0000000
312 Cxcl10 -6.473384 1.499039 0.0000000 0.0000000
329 Creb1 -6.520628 1.319746 0.0000000 0.0000000
360 Gpr34 -6.598321 1.362967 0.0000000 0.0000000
366 Mmp9 -6.620610 -1.820861 0.0000000 0.0000000
374 Sstr3 -6.648442 1.054868 0.0000000 0.0000000
392 Ccl4 -6.703674 1.065478 0.0000000 0.0000000
407 Glp2r -6.731767 1.857446 0.0000000 0.0000000
409 Nmbr -6.732447 -1.178506 0.0000000 0.0000000
415 Pf4 -6.747865 2.482443 0.0000000 0.0000000
416 Cdh9 -6.747917 -1.952098 0.0000000 0.0000000
444 Ntf3 -6.817653 1.189117 0.0000000 0.0000000
445 Tacr2 -6.822592 -1.620228 0.0000000 0.0000000
450 Smim40 -6.876962 1.632777 0.0000000 0.0000000
451 Cd83 -6.881214 -1.071720 0.0000000 0.0000000
461 Crhbp -6.972868 1.594353 0.0000000 0.0000000
464 Cd74 -7.002795 2.175515 0.0000000 0.0000000
467 Nts -7.005430 -2.521210 0.0000000 0.0000000
473 Chrna6 -7.057918 -1.430947 0.0000000 0.0000000
487 Ndufa4l2 -7.496608 -1.769197 0.0000000 0.0000000
497 Nr4a1 -9.347099 1.643357 0.0000000 0.0000000
499 Pdlim5 -9.662149 -1.716220 0.0000000 0.0000000

3.4.6 4 month, Endothelial Cell, SD v.s. nSD

Differentiation Gene List
names scores logfoldchanges pvals pvals_adj
0 Fam107a 19.874052 1.065273 0.0000000 0.0000000
2 Ccn2 15.399264 1.441248 0.0000000 0.0000000
8 Glp2r 9.531479 1.060113 0.0000000 0.0000000
13 Slc17a6 9.249908 -1.103294 0.0000000 0.0000000
17 Chrna5 9.096661 -1.429857 0.0000000 0.0000000
19 Mmp9 9.083175 3.424738 0.0000000 0.0000000
23 Cd74 9.011826 -1.521726 0.0000000 0.0000000
32 Fosb 8.949168 1.762628 0.0000000 0.0000000
36 Pf4 8.912031 3.446723 0.0000000 0.0000000
37 Ddit4l 8.901031 1.158544 0.0000000 0.0000000
44 Cox6a2 8.845735 -2.043570 0.0000000 0.0000000
47 Prlr 8.817331 -1.035781 0.0000000 0.0000000
50 Pde11a 8.779046 2.390600 0.0000000 0.0000000
57 Crhbp 8.751113 -1.568565 0.0000000 0.0000000
73 Chodl 8.679147 -3.851726 0.0000000 0.0000000
80 Gpr34 8.650617 -2.074064 0.0000000 0.0000000
85 Myh8 8.643071 1.391131 0.0000000 0.0000000
87 Synpr 8.641652 -1.017511 0.0000000 0.0000000
89 Calb1 8.629130 2.724319 0.0000000 0.0000000
100 Tnik 8.593813 -2.682249 0.0000000 0.0000000
128 Oxtr 8.510808 -1.871940 0.0000000 0.0000000
167 Ddit3 8.385195 -1.184006 0.0000000 0.0000000
172 Ntf3 8.377304 1.601173 0.0000000 0.0000000
189 Mas1 8.318790 -1.431413 0.0000000 0.0000000
244 Nrn1 8.021533 -2.507592 0.0000000 0.0000000
285 Fam180a 7.599267 -2.961184 0.0000000 0.0000000
290 Chrna6 7.573919 -1.116299 0.0000000 0.0000000
319 Cdh12 7.087206 -1.959252 0.0000000 0.0000000
320 Nectin3 7.083893 1.059902 0.0000000 0.0000000
392 Tcf7l2 3.595046 1.611849 0.0003243 0.0003596
471 Myh11 -7.580773 -1.301425 0.0000000 0.0000000
478 Cd9 -7.912252 1.199129 0.0000000 0.0000000
481 Kcnj8 -7.961404 3.697018 0.0000000 0.0000000
496 Cx3cl1 -10.129641 -1.055339 0.0000000 0.0000000

Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic